In order to determine if these Argonaute genes are required for heterochromatin formation, we utilized transcriptional reporters and ChIP of HP1 from somatic head tissue to monitor the heterochromatic state of piRNA clusters, which generate both endo-siRNAs and the bulk of piRNAs. Surprisingly, we find that mutation of AGO2 or piwi increases silencing at piRNA clusters corresponding to an increase of HP1 association. Furthermore, loss of piRNA production from a single piRNA cluster results in genome-wide redistribution of HP1 and reduction of silencing at a distant heterochromatic site suggesting indirect effects on HP1 localization. Taken together, these results indicate that heterochromatin forms independently of endo-siRNA and piRNA pathways in Drosophila somatic tissues. Our results indicate that heterochromatin can form independently of these two small RNA silencing pathways and appears to be achieved by alternate mechanisms in Drosophila and perhaps other metazoans. To further elucidate the role of Argonaute proteins in the higher order chromatin function, we performed ChIP followed by Illumina sequencing on an ovarian somatic follicle cell line. Our analysis revealed no association of Piwi with euchromatin but enrichment at highly repetitive sequences. In contrast, AGO2 localizes primarily with euchromatic sites throughout the genome.